which statistic method to use for DESeq

elisadouzi · 10-03-2011, 05:42 PM

I'm comparing the DEG between two very similar sample. They are just come from same plant but selfing independently 10 years. Which statistic method is appropriate for DESeq?

Thanks a lot!

NicoBxl · 10-04-2011, 12:28 AM

DESeq is a statistic method based on a non-binomial distribution. You've to used the raw reads as input. The best is to read the Simon Anders's paper on it : http://dx.doi.org/10.1186/gb-2010-11-10-r106

and the package doc : http://bioconductor.org/packages/rel...tml/DESeq.html

elisadouzi · 10-04-2011, 09:31 AM

Thanks for the reply

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10-03-2011, 05:42 PM	#1
elisadouzi Member Location: US Join Date: Mar 2011 Posts: 20	which statistic method to use for DESeq I'm comparing the DEG between two very similar sample. They are just come from same plant but selfing independently 10 years. Which statistic method is appropriate for DESeq? Thanks a lot!

10-04-2011, 12:28 AM	#2
NicoBxl not just another member Location: Belgium Join Date: Aug 2010 Posts: 264	DESeq is a statistic method based on a non-binomial distribution. You've to used the raw reads as input. The best is to read the Simon Anders's paper on it : http://dx.doi.org/10.1186/gb-2010-11-10-r106 and the package doc : http://bioconductor.org/packages/rel...tml/DESeq.html

10-04-2011, 09:31 AM	#3
elisadouzi Member Location: US Join Date: Mar 2011 Posts: 20	Thanks for the reply